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. 2021 May 24;12:3074. doi: 10.1038/s41467-021-23245-2

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© The Author(s) 2021

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 1 — a The intestinal tissue is suboptimally dissociated to generate clumps. b Clumps are enriched with FACS, based on Hoechst DNA staining; the histogram shows ImageStream quantification of the clumps’ nuclear DNA content (n = 3 mice). Source data are provided as a Source data file; bottom shows an example of a pair (left) and a 4-cell clump (right). Scale bar, 10 μm. c The position of clumps is computationally inferred by the enterocyte transcriptome, and spatial landmark genes for specific secretory cells are retrieved. d These are used to infer the location of single sequenced secretory cells, enabling zonation reconstruction.